Evangelion 2: Rebuild (Q) – The Changing of Instrumentality
by NotShinji
Summary: After Kaworu died in Unit-13, Shinji's emotions flared in an attempt to save him and succeeded in causing Fourth Impact, destroying the world. But when Shinji is offered the chance to return to life shortly before his life at NERV, he takes the chance in an attempt to make things right. With his knowledge of events, Shinji dives back through time to prevent SEELE's plans!
1. Happiness Can Be Found in Death

Evangelion 2: Rebuild – The Changing of Instrumentality

After Kaworu Nagisa had died in Unit-13, Shinji Ikari's emotions flared to an extreme amount in an attempt to save him and once again unknowingly tried and succeeded in causing Fourth Impact. As a result, the world was destroyed.

But when Shinji is offered the chance by the heavens to return to life shortly before his life at NERV began, he jumps at the chance in an attempt to make things right.

Using his knowledge of events and his alliance with Rei and Kaworu, Shinji dives back through time in order to save those he holds dear by preventing SEELE's and his father's plans!

* * *

Chapter 1 – Happiness Can Be Found in Death

Shinji woke up to a faint glow of blue light floating in the middle of dark nothingness. As he stands up and began to walk towards the blue light, he begins to ask himself questions.

'Am I still inside the cave?'

'Am I in a cell?

'Am I… Dead?'

Shinji began to make assumptions after he walked further towards the light. From what it illuminated, there were no walls in sight and there was no floor to walk on.

He wasn't even on solid ground anymore, so he made the assumption that he had indeed died and was in what people considered 'The Afterlife'.

Shinji logically wanted to cry and mourn his own death, but he just couldn't. He felt in his soul that the time had come, and so he no longer complained.

He no longer complained about his life in the EVA.

He still felt responsible for Near-Third Impact, even if he didn't know the consequences of what he had done at the time.

And yet, the one thing that he was responsible for that hit him the most, Kaworu Nagisa. After he was revealed to be the salvaged soul of Adam and therefore the 13th Angel, he tried to prevent Fourth Impact by using the explosive collar he took off Shinji and committed suicide.

However, it turns out his death was in vein, and as Shinji cried his heart out at the death of the one person who had truly accepted him as the world was slowly torn apart.

"And you plan to forever blame yourself for the death of your friend, let alone the world?"

Shinji was temporarily blinded by a bright light, and when he could, he opened his eyes to see the darkness replaced with endless skies and clear water he could walk upon.

Soon after this happened, a large crimson red bird flew from the sky down towards his location. When it reached the 'Ground', it transformed in front of his eyes into a woman who Shinji had thought looked familiar to Asuka.

The woman's hair reached down her back to waist length, where it rested nicely. She was naked, with her delicate areas not covered in the slightest as if to show she was not afraid of who she was.

"Hello, Shinji-Kun. It's been a while."

Shinji tried to look up towards the woman, but due to having respect and modesty he could not bring himself to look at her naked form and instead looked down towards his feet…

…only to find that he was also naked. He squealed and proceeded to cover up privates.

"Don't be afraid, Shinji-Kun. All Lilin were born like this, so it's natural that they look like this in the afterlife." The young Ikari looked into the woman's blue eyes and finally had the chance to bring words to his lips.

"Just hit me. I'm not afraid of anything anymore, Asuka-Chan."

The woman then proceeded to giggle before flowing into a full-blown bout of laughter. As she collected herself together she spoke; "I'm not THAT Tsundere, Shinji-Kun. And I'm not Asuka-Chan, even if we do look similar."

The woman then began to walk closer to Shinji and said; "Look at my eyes, Shinji-Kun."

Shinji stared into her Irises long before he noticed that they were of a golden colour, too un-natural even when compared to Rei's crimson red.

"Hmm… Now I think about it, it may be a good idea to put some clothing on after all." And with a flick of her wrist, the woman had slowly materialised a White Kimono around herself. Shinji then felt heavier, and noticed he was now wearing his regular school uniform.

"That's much better for you. Now, I really should introduce myself."

"I am Phoenix, the 19th angel that controls the Afterlife, and the wisest of all existent angels."

"Wisest? Don't take offense from it, but I never thought that Angels even possessed intelligence." Shinji was honestly surprised about this revalation, eager to learn more of it.

"None taken. I could tell you a lot of things that would make you regret your actions, but for the sake of your psychology I'd rather not. But all we ever wanted as Angels was to reunite with Lilith."

Shinji began to feel bad for the actions he "Decided" when it came to the angels. "Li-Lilith?"

Phoenix nodded. "Yes. While she did betray Adam, we are all children in comparision to the mighty two, eagerly wishing our "Parents" would come back together. But we knew that wasn't going to happen, and so when "Father" sent us down to "Mother", we wanted to be happy and reunited all over again."

"So until she fell apart from your father, you were all one big happy family?"

Phoenix then sadly smiled at Shinji. "Yes. I know you feel regret for your action but at the end of it, you never would have had a choice."

Shinji smiled sadly "It's OK. I'll just have to liv- I mean; Die with those consequences."

Phoenix put a hand on his shoulder from her current position. "You don't have to. They're all waiting. And while it may be uncomfortable for you, they'll forgive you for it. I'm sure."

Shinji felt better at this information, and smiled at the Angel. "T-Thanks, Phoenix-Sama."

Phoenix then crossed her arms and pouted at him, a solitary index finger wagging back and forth as if to tell him he knew no good. "Now come on, call me Phoe-Chan. I hate formalities."

"Okay… Phoe-Chan." Shinji smiled at her as he said this.

And likewise, Phoenix had smiled back at him.

"I said it's been a while… You obviously don't remember me after all those previous deaths…" She had spoke up to clear up the silence.

Shinji's face turned to a look of fear. "I-I've died before?"

"Oh boy, Shinji-Kun. I could count a few of yours, but I can think of something much better…"

She then materialised a television from the fabric of space they were in and showed the many deaths Shinji had faced since his time at NERV. From as early as being crushed by Sachiel on Day 1 and not being accepted by Unit-01, to as late as his battle against his father, to even more awkward and unfortunate deaths such as asphyxiation from Asuka where she held his nose when kissing him, ingestion of Misato's fatal cooking and the most ridiculous and embarrassing, drowning from the LCL that flooded into Unit-01's Entry Plug.

He was then shown another death, one that was powerful enough to upset Shinji to the point where he screamed at Phoenix to turn off the footage projected on-screen.

Shinji's instigation of Near-Third Impact, where he couldn't even reach for Rei and he watched her suffer as the world was destroyed. And his current death where he watched Kaworu explode in front of his eyes and Fourth Impact could not be prevented.

"Shinji-Kun! Shinji-Kun! They're in a better place now, they're OK-"

"NO! NOO!" Shinji wailed in mourning for his friends. "They died! They died in front of my eyes because I couldn't save them! Because I couldn't be the sacrifice! Why would you show me this? In fact, why even show me these?!"

"Shinji-"

"-Ikari-Kun."

Shinji froze and violently began shaking. He hadn't heard both of those voices since a very distant yesterday.

He turned around to see the face of multiple people he once knew from Pre -Third Impact. But there was two out of the group that stood out from the rest.

Rei Ayanami, the woman he had tried to save and instead almost destroyed the world.

Kaworu Nagisa, the best friend who had placed the explosive collar on his neck to sacrifice himself in an attempt to prevent the Fourth Impact.

The salvaged soul of Adam being the one friend who showed him true happiness.

And the woman that he had fallen in love with since the fight with Ramiel.

"…Ayanami-Chan? Kaworu-Kun?" Shinji began to cry tears of joy as he ran towards them with arms open wide, in which his friends followed suit.

The moment they were in arms distance, they embraced each other deeply as they all cried with tears of joy, the friends reunited.

Rei was the first to speak. "We're here for you, Ikari-Kun. Always."

"I… I couldn't save you. I tried to save you, and-" Shinji was silenced by Rei's index finger pressed softly against his lips as she shushed him.

"I forgive you. You tried to save me and that is all that matters, Ikari-Kun."

Shinji nodded in response to Rei, but still felt responsible for Kaworu's tragic end.

"And you died in vain. You literally stuck your neck out to get blown to pieces only for me to die-"

"I knew it would happen. I'm an Angel, so I just know these things. Besides-"

"They could never hate you, Shinji-Kun. Never." Shinji looked up to see the face of a woman in about her 30's, with short brown hair longer than Rei's by about 2 inches.

It took some time for him to realise. "M-Mother…?" The tears began to build up in Shinji's eyes.

The woman could only nod and say; "My son."

His friends had cleared the space between them in preparation for probably the greatest mother-son reunion in a while.

Yui had spoke up; "I've been watching you this whole time. When I was vaporised within Unit-01, I became part of it's neural network. I've been protecting you since the day you first stepped into the Entry Plug."

Rei was astonished. "…So you were Berserker all along?"

Yui simply nodded with a smile.

Shinji looked around at the mass group of friends that knew him. "Well, I've never had to deal with a situation like this before."

Rei just smiled. "Well, you could start by smiling. Then I'm sure Phoe-Sama could give us all a bit of time together at some point."

Shinji just smiled, recognising the reference to their time in the Entry Plug after the battle with Ramiel.

He looked into her crimson red eyes and then Kaworu's pair, and smiled. Not a forced one, but a genuine smile. Shinji had found happiness again, in the arms of his old friends.

"I missed you both." Shinji had held the two of them close together in a three-way hug, before with were interrupted by Phoenix.

"Shinji, I want to take you somewhere. Are you two coming?"

The pair looked towards the Angel of the Afterlife as she opened a portal to an entirely new landscape.

"Let's go, Shinji-Kun. The others will wait for us back home."

Another bright light flashed, opening a portal to the area Phoenix had mentioned. As Shinji and company waved goodbye at the remaining people, they slowly followed the 19th Angel through the portal.

* * *

They now stood upon the mountain overlooking Tokyo-3. The wind blew in Shinji's face, that familiar feeling he hadn't felt since he ran away after defeating Shamshel, the 4th angel.

"Tokyo-3 was destroyed in the Third Impact… How does this event exist?"

"We've gone back in time to a moment where Tokyo-3 still exists. It lives in the past now Shinji, but you can change the future… If you are willing."

Shinji was confused. "Hold on. So we've gone back in time… Because you want me to change it?"

Phoenix nodded. "But only if you want to. I can give you a month at the least to spend some time with the people in the city of Valhalla, but any longer and we won't stand a chance against the imminent danger the heavens will face."

Rei looked in fear towards Phoenix. "…We're in danger?"

"Indeed. I'm sure you all know about the Human Instrumentality Project."

Shinji wanted to know what they were talking about. "The 'Human Instrumentalilty Project'?"

Phoenix nodded. "Kaworu, if you would please."

The Angel smiled. "Yes, ma'am. The Human Instrumentality Project is the plan SEELE devised to sacrifice all Lilin in the Third Impact. But by finding safety in Lilith's egg, the leaders would become one godlike entity that would rule the remains of life for all eternity."

Shinji was intrigued by this new discovery. "And is it possible for it to happen?"

Kaworu then stated; "Nobody is sure. According to Phoenix, there was one alternate reality where Rei had awakened Lilith and started Third Impact to prevent Commander Ikari's desires for the Human Instrumentality Project. From what we could tell, only you and Pilot Sorhyu had survived."

Phoenix then jumped into the discussion. "There is a possibility that the Instrumentality could affect the heavens as well as all life on Earth. But we cannot be certain for sure. All I can tell you is that if it does work, except the apocalypse to happen and the rejected dead to walk the earth for all eternity."

Shinji understood the situation of the danger the universe was in. "I understand the situation, but what does it have to do with me?"

Kaworu then pitched back into conversation. "SEELE follows the fate they are given by a series of document of Extraterrestrial Origin known as the Secret Dead Sea Scrolls. They use these to predict their future and what they should do next."

Phoenix then chalks back into the conversation. "To put it simply, we want to give you another chance at making things right by defying the laws of the Secret Dead Sea Scrolls, not only preventing SEELE plans but also that of your father's."

Rei went back to state the main points of the conversation on everyone else's behalf. "We're at just as much risk from Instrumentality as much as those in the living are. You're our only hope, Ikari-Kun."

Shinji took a minute for it all to sink into his head.

"S-So wait, let me get this straight. All of mankind is at risk from Instrumentality and somehow I have to be the one who changes the fate of humanity?"

Phoenix nodded. "You won't go alone. Rei and Kaworu will go too in order to make sure you succeed in your quest."

Shinji thought about it. The idea that he could go back with his best friends to change the events that occurred at NERV would give him that second chance he always wanted. Plus if the heavens were indeed in possible danger, Shinji would rather not want to bear the burden of being the 'Destroyer of All Life'.

"I'll give you that month's time to fit in around here and make your decision-"

"I'll do it." Phoenix looked surprised and turned to see Shinji's face of determination, surprised that the once troubled teen was now prepared to make a stand in the name for what is right.

"Whether I go alone or not, I'll defy the Secret Dead Sea Scrolls and prevent Instrumentality."

And for once, Shinji was 100% sure that he would not run away.

* * *

END OF CHAPTER 1

Reviews? Like some other authors out there, we need constructive criticism and enough support and interest to continue our work.

I'm saying this in a nice, professional manner. I'd love your input because I'd probably not continue with this otherwise.

Ja Ne,

NotShinji


	2. Filler Chapter 1: The Mountain Picnic

Evangelion 2: Rebuild (Q): The Changing Of Instrumentality

Filler Chapter 1: The Mountain Picnic

After they left the mountain overlooking Tokyo-3, they decided to return to the others.

"Shinji-Kun" Phoenix had gained his attention and was now listening; "What you will see once we return to the heavens must remain a secret to the heavens and the heavens only. Not only would the idea of you three being time-travellers would make you instant mental asylum patients, but if the existence of the heavens is proven to the overworld people might start buying stairways to heaven looking for their dead ones."

Kaworu began to laugh. "Nice little joke you put in there. Not often do you find someone up here with a taste in classic rock music, either."

"Well what can I say? I've always loved a bit of Led Zeppelin every now and then. Good when you need to clear your head."

Shinji didn't get what in the heavens they were on about. "Uh, guys. Explain?"

Rei jumped in, pulling her pair of earphones out to explain. "Led Zeppelin are a famous rock band from the west. Stairway To Heaven which Phoenix quoted was considered one of their best songs, but I think they did better. Like Kashmir or Immigrant Song."

Shinji's face was just confused. "Wha…?"

Rei just rolled her eyes, gave him her SDAT and told him to listen to tracks 5-7 on her custom tape she made for outings. He just walked along the mountainside listening as they all took a pleasant walk together. Nobody bothered anyone until they reached the desired spot, a clearing at the top of the mountain with a small cherry blossom tree in the middle of a clearing. Not too far off was a view of Tokyo-3 and it's surroundings.

"Well, we made it!"

Phoenix then sat down and materialised a portal with which she pulled out a picnic basket. After closing the portal, she opened up the bag to reveal enough food for everyone to share together.

"Lunch is served!" Phoenix had shouted in joy. The blanket was placed over the dew of the grass left from earlier that morning, staining the bottom of the fabric and taking in the scent of the fresh air.

The rest of the group took a seat and all did their own things. Shinji had decided to cloudwatch from his position laid backwards on the fabric, while Rei was close to him listening to the music coming through the earphones attached to her SDAT.

Phoenix was cuddled up to Kaworu, both of which were now asleep in each other's arms.

"I missed you. I missed you so much." Shinji could hear as he paid attention to the source of the noise.

There was Rei, looking directly into his eyes with a hand extending itself from her chest to his.

Shinji decided to move up closer to snuggle into each other's body warmth.

"Have you ever thought about what you wanted to do for your future, Ikari-Kun?"

"You still call me Ikari-Kun after all this time?" Shinji teased her about the use of last names and she blushed.

"You know, it's okay to call me Shinji-Kun… Actually, I think it would be better for the both of us, Rei-Chan."

Her face widened in surprise before smiling and saying; "OK, Shinji-Kun."

He brought her closer so that she was resting on his chest. As they got closer and closer to falling asleep, Shinji eventually answered her question from earlier.

"I want to settle down, Rei-Chan. I want to get married, have children if my lover can and live a successful and supportive lifestyle. But we have forever to decide now. What about you?"

Rei looked up to his face and spoke. "I don't really know. I know I would probably find a job and settle into that, but I… I just don't want to be alone at the end, that's all. I want to be in the arms of someone who could kiss me awake in the morning and make me a cute breakfast and… All the other fluffy stuff you've supposed to do as a couple."

Shinji smiled. "Do you think you'll find someone that will, someday?"

Rei just snuggled further into him, humming a quiet yes. Snuggled into each other as they fell asleep, Rei last thoughts before she snoozed off were;

'_I've already found him… I found him long ago. But would he accept me as a person now? …Or would he push me back for having changed so much?'_

She could only think and ponder those thoughts as she drifted off to a peaceful sleep.

END OF FILLER CHAPTER 1: THE MOUNTAIN PICNIC


	3. Love Once Lost, Now Earned

Evangelion 2: Rebuild (Q): The Changing Of Instrumentality

Chapter 2: Love Once Lost, Now Earned

* * *

Shinji opened his eyes to find himself no longer on a hill looking at the skies, but at a simple blank ceiling. Completely ignoring this factor, he lifted himself up in bed, taking in his surroundings.

His bed was queen-sized and made for two people, and was placed in the center of the room similar to the layout of a general hospital room. Two dressers were to his direct left and right, suggesting that this room was intended to be shared between two people. Shinji deduced from these factors that this room was made for a couple.

As he took in all of the details around him, Shinji noticed that he was wearing his sleeping attire. This confused him, as he had fallen asleep upon the hill with Rei in his usual uniform and—

Wait.

Shinji paused at this thought. Did that really happen? The room he was in itself reinforced this thought, sure. But he has woken up before in somewhere completely different from his previous position.

He looked up, and the same comment like every other time was said. This time however, with a touch of humor.

"Another unfamiliar ceiling. I seem to get used to this everytime…"

Shinji then tilted his head down, looking at the hand which Rei's tears had dripped onto during their reunion.

"…Still though, It felt so real…"

"…Because it was real."

He lifted his head to the source of the voice.

There he saw Rei, wearing a short and simple white nightdress that ended midway down her thighs. He blushed at the clothing she wore, noticing how revealing the attire was.

Completely innocent and unaware, Rei walked beside him and sat on the previously empty side of the bed.

"You look a bit confused, Ikari-Kun."

Shinji gave a mild chuckle and a small smile. "Well, it's to be expected when you have a weird dream of meeting your dead loved ones in the afterlife…"

The Bluenette just snuggled up to the brunette pilot's person, laying on the bed. Surprised by how bold Rei had actually become, he eventually rested his head back on the pillow.

"When did you get all soft on me?"

Rei just blushed, her pale face now a vibrant pink.

"By the way, I appreciate your help in trying to get me and dad to bond… Sorry your life ended the way it did. It's my fault-"

Shinji was interrupted by Rei placing an index finger over his lips and leaning closer to him. "It was never your fault, Shinji-Kun. I made the mistake that day of attacking Zeruel with that missile, not knowing it would not do anything. It's my fault." She looked at the bed in guilt.

Shinji took his hand and raised her face. "Hey! As you just said, you didn't know the consequences. I don't blame you for anything, either. You did great, but eventually something will have to get the better of us sometime."

Rei just smiled. And even though he was focused on her smiling face and her crimson red eyes, he could not help but notice the slight shiver she gave. Suddenly time-conscious once again, Shinji asked;

"How long do we have?"

"We have until 1000 hours to meet the 19th Angel of Life at the citadel. The time right now is 0715 hours… Why?"

Shinji thought; _'Perfect. Now's a good time more than any other.'_

"Do you want to climb in with me? You look freezing…"

Rei blushed before giving a slow nod. As he pulled the covers back, she cuddled up next to him and rested her delicate yet athletic frame upon his muscular and well-built one.

"...It's strange."

"Hmm?"

"…You were my first for a few important moments in my life. You were my first friend. You were the first person I thanked. The first person I wanted to do a good deed for… What I want to say is that… You make me feel warm inside…"

Shinji tried to speak, but could not find the right words for the situation except for two choices that he now mashed into one.

"…I feel the same, Rei-Chan."

She looked into his eyes as he casted his eyes to the ceiling.

"The feeling where to even see that person makes you happy. When you share the same emotions as them and whenever they go through an emotional time, you want to be there for them. When you want to be around them solely just to make sure that they are alright…"

No longer looking at the ceiling, Shinji now looked directly at Rei.

"…What I'm trying to get that is that feeling is love, Rei-Chan. A-And even if it's not the same as how you feel, I love you anyway."

Rei just looked at him, each staring into each others eyes.

"…Why do I feel like you deserve better than me?"

"Because we all make mistakes that we're not proud of. But I'm with you on whatever decision you decide to make…"

Rei broke the hug, leaning over Shinji who was watching her every move as she slowly placed her lips upon his as they expressed their emotions regarding one another in a kinetic matter.

After the kiss, Rei found the words she wanted to say with the greatest smile on her face.

"…I love you too… Shinji-Kun."

And soon again they were encased in another passionate liplock.

* * *

After waking back up from their passionate moment from earlier on, Shinji and Rei were just leaving the apartment building where Rei lived.

"Whoa…" He could not stop thinking about the huge size of half of the skyscrapers in front of his eyes

"Let's go, Ikari-Kun!" And in a flash, Rei had pecked his cheek and ran off with a blush.

"H-Hey, Rei-Chan! Get back here!"

Shinji proceeded to chase his now-girlfriend to the ground floor where he eventually caught up with her and picked her up, swirling her around and generally being a cute couple. When they stopped, they proceeded to walk hand-in-hand to the nearby train station and hitch a ride to the citadel.

Once they reached the main building, Phoenix was waiting for them at the corresponding elevator.

"Hey. Glad to see you two have finally sorted things out between yourselves." She had stated as the elevator opened, revealing Kaworu and another very familiar face.

"Shinji!" Lieutenant Captain Misato Katsuragi rushed out of the elevator to greet her old charge and roommate.

"Misato! It's been way too long!" Shinji embraced her and instantly recognised the scent of her favourite beer on her jacket.

"Well anyway you two, we all need to head upstairs if you don't mind… You can have your reunion later…" Phoenix had now moved into the elevator, which now occupied the rest of the group. The old roomies had slowly entered the elevator and went up the thousands of floors which took only a short amount of time to cover.

When the elevator reached the executive floor, Shinji stepped out and noticed the huge window. Looking outside, he was struck in awe.

The height of the Citadel was large enough that from this window, you could see everything that happened in the city. What looked like the entrance to the heavens was seen enrolling new citizens into the city, and the distance covered was enough to see the edge of the heavens, despite the fact that those who have all died were still housed within this floating land.

"What you see here Shinji-Kun is Sovngarde, the floating city of the heavens. It is your home now, and your job is to assist in it's protection and safety."

And with that, they all walked into Phoenix's office to discuss their situation.

* * *

END OF CHAPTER 2: LOVE ONCE LOST, NOW EARNED

Hi guys, NotShinji here;

Well actually I'm Shinjiikari1995 on Twiiter, which is a Roleplay account… So I actually AM Shinji. Hooray, whiny bitchass turned witty new commander of NewNERV. Awesome.

I've read the reviews from a few people, and I want to say thanks to those who have taken the time to Read and Review. Your constructive criticism is very helpful in my improvement as a writer, and so every comment is much appreciated.

My basic plans for the series involves Shinji having more of a backbone. Because he is also going back through time and knows about Human Instrumentality, the plan is that he will attempt to prevent SEELE's plans of using Third Impact to control all life and become gods.

Gendo Ikari (That's Papa Shinji to you) and his desires for Human Instrumentality are to actually bring back Yui, his dead wife and Shinji's loving mother. So I'll plan to use this to my advantage, but at either rate Shinji will tell his father that he knows the truth about his secret work. This should add some decent plot twisting, so keep 'em peeled!

Sovngarde: The land of the heavens. The term is heard in The Elder Scrolls V: Skyrim.


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